HLA-A, B, C, DR and DQ polymorphisms in three South African population groups: South African Negroes, Cape Coloureds and South African Caucasoids

Perspectives on establishing a public cord blood inventory in South Africa

The South African population is highly diverse, both ethnically and genetically. This diversity is particularly true for the African ancestry and various mixed ancestry population groups. These groups are under-represented in national and international bone marrow and peripheral blood donor registries, making it challenging to identify HLA-matched and mismatched unrelated donors when patients from these groups require allogeneic hematopoietic stem and progenitor cell transplantation. In most high-income countries, banked cord blood (CB) units provide an attractive source of hematopoietic progenitor cells for genetically diverse populations. SA does not have a public CB inventory, leaving many patients without access to this important treatment modality. Haploidentical transplantation provides an alternative. In recent years, the use of post-transplant cyclophosphamide has significantly reduced the incidence of graft-versus-host disease after haploidentical transplantation and has improved transplantation outcomes. However, it is difficult to identify suitable haploidentical donors in SA because of family disruption and a high prevalence of HIV. Here the authors provide a brief historical overview of the ethnic and genetic diversity of the country and region. The authors provide a southern African perspective on HLA diversity, consider the allogeneic hematopoietic stem and progenitor cell transplantation landscape and explore the need to establish a public CB bank (CBB) in SA. The health policy and regulatory frameworks that will impact on a CBB in the country SA are also explored. Finally, the authors discuss several matters we believe require attention when considering the establishment of a sustainable public CBB in the South African context.

Population tailored modification of tuberculosis specific interferon-gamma release assay

Objectives

Blood-based Interferon-Gamma Release Assays (IGRA) identify Mycobacterium tuberculosis (MTB) sensitisation with increased specificity, but sensitivity remains impaired in human immunodeficiency virus (HIV) infected persons. The QuantiFERON-TB Gold In-Tube test contains peptide 38–55 of Rv2654c, based on data indicating differential recognition between tuberculosis patients and BCG vaccinated controls in Europe. We aimed to fine map the T cell response to Rv2654c with the view of improving sensitivity.

Methods

Interferon-gamma ELISpot assay was used in HIV uninfected persons with latent and active tuberculosis to map peptide epitopes of Rv2654c. A modified IGRA was tested in two further groups of 55 HIV uninfected and 44 HIV infected persons, recruited in South Africa.

Results

The most prominently recognised peptide was between amino acids 51–65. Using p51-65 to boost the QuantiFERON-TB Gold In-Tube assay, the quantitative performance of the modified IGRA increased from 1.83 IU/ml (IQR 0.30–7.35) to 2.83 (IQR 0.28–12.2; p = 0.002) in the HIV uninfected group. In the HIV infected cohort the percentage of positive responders increased from 57% to 64% but only after 3 months of ART (p = ns).

Conclusions

Our data shows the potential to population tailor detection of MTB sensitization using specific synthetic peptides and interferon-gamma release in vitro.

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Refined epitope mapping of Rv2654c was performed in a South African Xhosa population.

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The most frequently recognized peptide is p51-65 (VRAVAESHGVAAVLF).

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Using p51-65 in the QFT assay resulted in a significant boosting effect.

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Peptide p51-65 can improve the population tailored detection of MTB sensitization.

Bioinformatic and empirical analysis of novel hypoxia-inducible targets of the human antituberculosis T cell response

We analyzed whole genome-based transcriptional profiles of Mycobacterium tuberculosis subjected to prolonged hypoxia to guide the discovery of novel potential Ags, by a combined bioinformatic and empirical approach. We analyzed the fold induction of the 100 most highly induced genes at 7 d of hypoxia, as well as transcript abundance, peptide-binding prediction (ProPred) adjusted for population-specific MHC class II allele frequency, and by literature search. Twenty-six candidate genes were selected by this bioinformatic approach and evaluated empirically using IFN-γ and IL-2 ELISPOT using immunodominant Ags (Acr-1, CFP-10, ESAT-6) as references. Twenty-three of twenty-six proteins induced an IFN-γ response in PBMCs of persons with active or latent tuberculosis. Five novel immunodominant proteins-Rv1957, Rv1954c, Rv1955, Rv2022c, and Rv1471-were identified that induced responses similar to CFP-10 and ESAT-6 in both magnitude and frequency. IL-2 responses were of lower magnitude than were those of IFN-γ. Only moderate evidence of infection stage-specific recognition of Ags was observed. Reconciliation of bioinformatic and empirical hierarchies of immunodominance revealed that Ags could be predicted, providing transcriptomic data were combined with peptide-binding prediction adjusted by population-specific MHC class II allele frequency.

Human leukocyte antigen class I haplotypes of human immunodeficiency virus-1-infected persons on Likoma Island, Malawi

Human leukocyte antigen (HLA) allele frequencies vary between different human populations, with implications both for the evolutionary pressures shaping those populations as well as for the outcome of new infectious epidemics. We defined HLA class I types in a well-described cohort of persons on Likoma Island in Malawi, a population for which there are lacking data on allelic frequencies. The profile of HLA frequencies was similar but phylogenetically distinct from those of other sub-Saharan African populations in neighboring regions. The most common A alleles included A30, A23, A28 (A*68), and A2, and the most common B alleles included B15 (group), B53, B58, and B44. Notably, the frequency of B53, which is protective against malaria, was similar to that of other malaria-endemic African countries, and higher than that in countries with less malaria. This is the first reported significant dataset of HLA class I allelic frequencies in Malawians.

HLA class II disease associations in southern Africa

Southern Africa harbors several population groups representing a diversity of gene pool origins. This provides a unique opportunity to study genetic disease predisposition in these populations against a common environmental background. Human leukocyte antigen (HLA) association studies of these populations could improve knowledge on inter-population variation and HLA-related disease susceptibility. The aim of this paper is to review HLA class II disease associations reported for southern African population groups, compare them with findings in other populations and identify those unique to southern Africa. A number of HLA class II disease associations appear to be unique to southern African populations. These include DRB1*14011 association with insulin-dependent diabetes mellitus susceptibility in the Xhosa and DRB1*10 and DQB1*0302 with rheumatoid arthritis susceptibility in the South African (SA) Indian and SA Coloreds, respectively. A noteworthy similarity in class II disease association was observed among southern African Caucasoid and their European parental populations. Unique HLA class II disease associations observed in southern Africa are consistent with the notion that unique environmental and natural selective factors have resulted in certain ethnic-specific HLA class II disease associations, while common HLA class II disease associations found across different populations support the notion that common diseases are caused by common, ancient alleles present in indigenous African populations.

Thrombotic thrombocytopenic purpura in patients with retroviral infection is highly responsive to plasma infusion therapy

We prospectively studied presentation biological differences and the response to therapy in patients with thrombotic thrombocytopenic purpura (TTP) associated with, or unrelated to human immunodeficiency virus (HIV) infection. TTP patients underwent standard evaluations and were treated with prednisone 1 mg/kg in addition to infusions of fresh frozen plasma (FFP; 30 ml/kg/d) until normalization of the platelet count. Unresponsive patients were referred for plasma exchange. Compared with HIV- TTP patients (n=23), in HIV+ subjects (n=21) microangiopathy was dominant among Black females, who had lower presentation Hb (median 5.8 g/dl; P=0.03), platelet count (13 x 10(9)/l; P=0.05) and a CD4 count of 0.096 x 10(9)/l. HIV+ individuals responded to FFP faster than HIV- patients and none of them required apheresis. Ten HIV- TTP patients required apheresis (P=0.03) and four died. Responses in the HIV+ and HIV- groups occurred after treatment with a median of 33 and 55 units (one unit=320 ml) of FFP (P=0.004) respectively. Response to this protocol was seen in 84% (95% response in HIV+ patients). Regression analysis showed that survival was associated with younger age (P=0.001), rapid platelet (P=0.001) and Hb (P=0.0009) recovery, and fewer FFP units to normal lactate dehydrogenase levels (P=0.006). We conclude that in HIV+ individuals, microangiopathy is highly responsive to plasma infusions. This observation is important particularly when apheresis is not available.

Increasing dose intensity of anthracycline antibiotics improves outcome in patients with acute myelogenous leukemia

To understand the effect of dose concentration in the overall survival of AML, we conducted a study on the efficacy and toxicity of a drug combination where the dose of daunorubicin was intensified. For this analysis, the outcome of patients entered into two consecutive prospective trials was compared. Inclusion criteria in both arms were identical and consisted of primary AML in adults. Treatment protocol for Cape Town Regimen 4 (CTR-IV) comprised of cytarabine infusion (100 mg/m(2)) and etoposide (100 mg/m(2)), injection daily for 7 days in combination with daunorubicin (45 mg/m(2)) on days 1, 2, and 3. Patients achieving remission were given two further courses of the same chemotherapy and received allogeneic or autologous transplantation. CTR-V was a similar treatment program, except that daunorubicin was escalated on days 1, 2, and 3 to 75 mg/m(2) during induction and to 60 mg/m(2) during a single consolidation. Patients were also offered stem cell transplantation. Between 1990 and 1997, 78 patients (median age 33; range 13-67 years) fulfilled entry criteria and received CTR-IV. From 1998 onwards, 35 patients (median age 36; range 15-66 years) were prospectively enlisted into the CTR-V trial. The patient population in CTR-V had fewer Caucasian individuals (P = 0.02) and had significantly lower presentation hemoglobin (P = 0.0002). Following initiation of induction chemotherapy, 40 patients failed to respond. Among these, 10 patients demised before day 28. Another 30 (25/69 CTR-IV and 5/32 in CTR-V groups; P = 0.01) had leukemia that was resistant to chemotherapy, and all died. Remission was achieved in 59% of patients treated with CTR-IV and 77% of those receiving CTR-V (P = 0.03). CR occurred with a single course in 64% versus 88% (P = 0.02), respectively. There were no differences in the toxicity profile between these two combinations. Disease recurred in 50% and 28% (P = 0.07) of patients. For the 113 individuals, median follow up is 254 (range 19-4,451) and 304 (12-1,702; P = 0.03) days. Survival is 23% and 40%, respectively, favoring patients treated with CTR-V (log rank; P = 0.03). Cox regression analysis showed that treatment group (P < 0.001), FAB type, hemoglobin level, and platelet count were independent factors for response to chemotherapy. Older age and not undergoing myeloablative therapy were the only adverse factors for survival. We conclude that increase in the treatment dose of daunorubicin in patients with AML led to a higher remission rate, particularly with a single course of chemotherapy and had an equivalent toxicity profile. This therapeutic modification is also likely to result in substantial reduction in patient stay in hospital and in the overall expenditure.

Hierarchical targeting of subtype C human immunodeficiency virus type 1 proteins by CD8+ T cells: correlation with viral load

An understanding of the relationship between the breadth and magnitude of T-cell epitope responses and viral loads is important for the design of effective vaccines. For this study, we screened a cohort of 46 subtype C human immunodeficiency virus type 1 (HIV-1)-infected individuals for T-cell responses against a panel of peptides corresponding to the complete subtype C genome. We used a gamma interferon ELISPOT assay to explore the hypothesis that patterns of T-cell responses across the expressed HIV-1 genome correlate with viral control. The estimated median time from seroconversion to response for the cohort was 13 months, and the order of cumulative T-cell responses against HIV proteins was as follows: Nef > Gag > Pol > Env > Vif > Rev > Vpr > Tat > Vpu. Nef was the most intensely targeted protein, with 97.5% of the epitopes being clustered within 119 amino acids, constituting almost one-third of the responses across the expressed genome. The second most targeted region was p24, comprising 17% of the responses. There was no correlation between viral load and the breadth of responses, but there was a weak positive correlation (r = 0.297; P = 0.034) between viral load and the total magnitude of responses, implying that the magnitude of T-cell recognition did not contribute to viral control. When hierarchical patterns of recognition were correlated with the viral load, preferential targeting of Gag was significantly (r = 0.445; P = 0.0025) associated with viral control. These data suggest that preferential targeting of Gag epitopes, rather than the breadth or magnitude of the response across the genome, may be an important marker of immune efficacy. These data have significance for the design of vaccines and for interpretation of vaccine-induced responses.

Spondyloarthropathies in sub-Saharan Africa

HLA-B27 is virtually absent in most of the sub-Saharan Africa populations, and ankylosing spondylitis is rare; only a few patients have been reported from central and southern Africa. HLA-B27 was present in only one of 17 patients (6%). The disease shows clinical features that are similar to those observed in white HLA-B27-negative patients with ankylosing spondylitis; ie, the disease onset is later compared with HLAB27-positive patients, the patients rarely get acute anterior uveitis as one of the extra-articular manifestations, and familial occurrence of ankylosing spondylitis is rarely observed. There is a virtual absence of ankylosing spondylitis even in the west African countries of Gambia and Senegal, where 3% to 6% of the general population has HLA-B27. The epidemic of HIV infection in sub-Saharan Africa in recent years, however, has been associated with a dramatic upsurge in the prevalence of spondyloarthropathies other than ankylosing spondylitis, primarily reactive arthritis and undifferentiated forms of the disease, and less often psoriatic arthritis. HLA-B27, because of its rarity and virtual lack of association with the observed cases of spondyloarthropathy in this population, cannot be used as an aid to diagnosis of spondyloarthropathy in black Africans. Conversely, HIV infection is increasingly showing such a strong association with reactive arthritis, psoriatic arthritis, and undifferentiated spondyloarthropathies in sub-Saharan African populations that any patient with acute or chronic inflammatory arthritis may need to be tested for possible HIV infection. More research is needed on the evaluation of risk and protective factors in sub-Saharan African populations to better delineate the relative importance of genetic and environmental factors in the pathogenesis of spondyloarthropathies.

HLA-A and -B alleles in cornea donors as risk factors for graft rejection

We determined the human leucocyte antigen (HLA)-A, -B and -DR allele frequencies in recipients and donors of 115 cornea transplants, for recipients who developed graft rejection and those who did not. No difference in HLA allele frequencies of the recipients was found. The frequencies of the HLA-A26, -B35 and -B44 alleles in cornea donors were increased in recipients who developed graft failure. The detrimental effect on corneal graft survival of these alleles was significant (p < 0.001). No such effect was observed in renal transplantation. Corneal graft survival was similar when one or two A26, B35 or B44 alleles were present on the donor cornea. The negative effect was similar in magnitude to the previously reported negative effect of an HLA-B locus match between donor and recipient. When both a B-locus match and an A26, B35 or B44 allele were present, the negative effect on graft survival was twice as strong, indicating that different immune mechanisms are responsible for these phenomena.

A unique African HLA haplotype may identify a population at increased risk for kidney graft rejection

We determined HLA-A, -B, and -DR allele frequencies in kidney transplant recipients in relation to graft survival. Most recipients and donors were from African descent. The frequency of HLA-A30 was somewhat increased in recipients who rejected the graft. The frequency of HLA-B42 was significantly (P=0.002) increased in recipients who rejected the graft. Similar results were found for the HLA-DR3 allele; however, this effect was diminished when B42-, DR3+ individuals were analyzed. We further investigated the effect on transplant outcome of a unique African haplotype A30, B42, DR3, and of segments thereof, which have a high frequency in the local population. Log-rank analysis revealed that the negative effect on transplant outcome was least in A30-, B42+ recipients (P=0.417) and most pronounced in A30+, B42+ patients (P=0.006). We postulate that the negative effect on transplant outcome may reside in the A30, B42 segment of chromosome 6 and may be caused by a stronger than average immunoregulatory gene.

HLA class I and class II allele distribution in the Bubi population from the island of Bioko (Equatorial Guinea)

We determined the HLA frequency distribution in a sample of 100 Bubi individuals born on the island of Bioko (Equatorial Guinea). HLA-A, -B and -C typing was performed by serology and PCR-SSP. DRB1/3/4/5, DQB1 and DQA1 alleles were determined by PCR-SSOP. The HLA allele distribution of this population group resembles those found in other Bantu-speaking groups; however, the higher frequency of A30, A32, B44, DRB1*1301 in the Bubi with respect to other Bantu groups and the absence of DR4 deserve special mention. The cloning and sequencing of class I and II genes in this population allowed the description of five new allelic variants: B*4407, Cw*0706, Cw*1801, Cw*1802 and DQB1*0612 and five confirmatory sequences: B*3910, B*5703, B*8101, Cw*1203 and Cw*1701. The following new HLA-C,B haplotypes have been found in Bubi: Cw*08-B*57, Cw*18-B*57, Cw*0302-B*53, Cw*07-B*53 and Cw*1601-B*63. The most frequent seven-locus haplotype is: A*30-Cw*17-B*42-DRB1*1102-DRB3*0202-DQA1*05-DQB1 *0301. In terms of genetic distance, the Bubi are closer to other Bantu groups than to West African populations.

HLA-DR 52- and 51-associated DRB1 alleles in Kenya, east Africa

The genes of the major histocompatibility complex (MHC) are amongst the most polymorphic loci known in the human population. The population genetics of the MHC encoded HLA loci of sub-Saharan Africa are of major interest because of their particular genetic diversity. Here we report on the HLA-DR 52- and 51-associated determinants of the DRB1 loci observed in 165 East African individuals studied in Nairobi, Kenya. The HLA-DR typing was done by serologic and by molecular DNA techniques (PCR-SSOP). The most frequent allele identified was DRB1*1101, followed by DRB1*1503 and DRB1*1302. Some unexpected alleles were repeatedly identified: DRB1*1108, DRB1*1316 and DRB1*1421. Most of the DR 52- and 51-associated DRB1 alleles were correctly identified by serology as part of the DR3, DR5, DR6 and DR2 groups respectively. The HLA-DRB1 profile reported here corroborates previous genetic and linguistic data supporting the concept that the Eastern African Black population is genetically distinct from other African Black populations. This has important implications in public health issues related to the genetic profile of a population (transplantation, vaccine design for example).

HLA-A, -B, -C, -DR, -DQ typing in a population group of Senegal: distribution of HLA antigens and HLA-DRB1*13 and DRB1*11 subtyping by PCR using sequence-specific primers (PCR-SSP)

One-hundred-and sixteen Senegalese Serere were typed for HLA antigens and compared with other ethnic groups in Gambia. We did not find significant differences (Fisher's exact test; P < 0.01) in the HLA antigens distribution between the Serere and Mandinka groups in Senegal and the Serere, Mandinka and Wolof in The Gambia. The most common HLA haplotypes found (P < 0.01; Chi square with Yates' correction) were: A1, B8; A2, B51; A32, B44; A33, B58; A2, Cw2; A2, Cw4; A33, Cw3; A2, DR17; A10, DR10; B35, Cw4; B53, Cw6; B57, Cw3; B65, Cw8; B50, DR15; B52, DR4; Cw2, DR17; DR7, DQ2; DR18, DQ4. The HLA-DRB1*13 and DRB1*11 alleles were subtyped by PCR-SSP and the frequencies of these alleles in the studied population given. HLA-DRB1*1304 and DRB1102 were the most common alleles found respectively 15.0 and 18.5%.

Distribution of HLA and haplotypes of Colombian and Jamaican black populations

To investigate the genetic background of the black populations of Colombia and Jamaica, we determined HLA types of 78 Colombian and 98 Jamaican blacks from 2 different socioeconomic groups (Jamaican #1 and Jamaican #2) and estimated the frequencies of HLA genes and haplotypes. A phylogenetic tree based on the HLA gene frequencies revealed that Jamaican #1 and Jamaican #2 were distinct from each other, Jamaican #1 being closely related to the Colombian blacks and the Jamaican #2 being closely related to Senegalese and Zairean populations. Three-locus HLA haplotypes of Colombian and Jamaican #1 blacks were an admixture between Africans and Caucasians or South American Indians, while Jamaican #2 blacks were relatively homogeneous and appeared to conserve African lineages. The major five-locus HLA haplotypes were not shared among Colombian, Jamaican #1 and Jamaican #2 blacks. These results indicated that the black populations of Colombia and Jamaican were originated from African blacks and admixed variably with Caucasians and South American Indians to make genetic subpopulations in Colombia and Jamaica.

Structural diversity in the HLA-A10 family of alleles: correlations with serology

The HLA-A10 crossreacting group consists of the A25, A26, A34, A43 and A66 antigens. Here, we report allelic sequences for A43 and for 2 subtypes of both A26 and A34. Combining these results with previously determined sequences for A25, A26 and A66 enables molecular comparison of all the serologically defined A10 antigens. They form a closely related and well-defined group of alleles which may have originated with A*2601. Patterns of serological crossreactivity are correlated with sequence and a public epitope shared by A33 and members of the A10 family is localized to residues R62 and N63. The A*2501, A*4301 and A*6601 alleles appear to have derived from A*2601 by single gene conversion events with other HLA-A alleles. In the case of A*4301, the donor allele was probably an A29 allele as A*4301 has a small element of sequence in the alpha 1 helix (residues L62 and Q63) uniquely shared with A29. The chimaeric structure of A43 explains the reactivity of A43 molecules with both A10 and A29 alloantisera. The rare Oriental variant of A26 (A26v*) is encoded by an allele (A*2602) that differs from A*2601 by a unique nucleotide substitution which changes aspartate to asparagine at position 116 in the floor of the peptide binding groove. Thus A*2602 is a functionally distinct allele that originated by a point mutation. Alleles encoding A34 and A66 antigens are found to have very similar structures, explaining the difficulty in their serological definition.(ABSTRACT TRUNCATED AT 250 WORDS)

Extensive genetic diversity in the HLA class II region of Africans, with a focally predominant allele, DRB1*1304

Molecular HLA class II typing of greater than 1700 individuals from The Gambia in West Africa and Malawi in South-Central Africa revealed a striking diversity of HLA DRB-DQB haplotypes as defined by restriction fragment length polymorphism (RFLP); this diversity is twice as extensive as that found in northern Europeans. Despite this diversity, sequence and PCR/oligonucleotide analysis showed that the recently described variant DRB1*1304 is the commonest DRB1 allele in The Gambia. The sequence, geographical distribution, and RFLP association of this allele, together with homozygosity test results, suggest that DRB1*1304 may have arisen from DRB1*1102 and have reached its remarkably high frequency as a result of recent directional selection. The prevalence of this unusual allele has implications for trials of subunit vaccines in this area. The extensive and distinctive HLA class II region polymorphism in sub-Saharan Africans is consistent with evidence from other genetic loci implying an African origin of modern Homo sapiens.

HLA alleles in the population of Cartagena (Colombia)

It is known from historical records that the population of Cartagena (Colombia) is a mixture of caucasoids (Spaniards) and negroids (Africans) that is named mulattos. The present study was carried out to determine the distribution of HLA antigens in this population. A sample of 370 individuals was HLA serologically typed; 91 of them were typed for Complement alleles and 47 were DNA typed using PCR amplification and oligonucleotide probes for the HLA-DQA1 locus. The analysis of the allele and haplotype frequencies obtained, together with the genetic distances calculated with other populations, showed that most of the HLA genes of mulattos are from negroids and caucasoids. The Asian and Amerindian contribution is small, consistent with the historical and socioanthropological documentation. For example, A23, Aw34, Aw36 and Bw45, as well as DQA1*0101, DQA1*0301 and BfF have frequencies similar to that observed in negroids. In contrast, many significant differences were observed when comparing the antigen and allele frequencies of mulattos with that of Asians and Amerindians. Our results add evidence to the notion that the arrival of Spaniards in America 500 years ago established several racial mixtures. The HLA characterization of one of these, mulattos, will allow a better application of the HLA technology in the fields of basic research, organ transplantation and forensic medicine among this population.

Analysis of HLA-DR and -DQ gene polymorphisms in Sudanese patients with type 1 (insulin-dependent) diabetes

In this study we report for the first time, the molecular analysis of HLA-DR and -DQ gene frequencies in a large cohort of well characterized type 1 (insulin-dependent) diabetes mellitus (IDDM) patients (n = 72), and ethnically matched controls (n = 59) collected in sub-Saharan Africa. High molecular mass DNA was prepared and analyzed in Southern blots with DRB1, DQA1, and DQB1 probes. By identifying DR and DQ allele-specific restriction fragment length polymorphisms (RFLPs), we have shown a strong positive association between IDDM and the Asp 57- DQB1 allele *0201 (DQw2). A rare DR4, DQw2 haplotype was also identified at high frequency in the IDDM cohort. We can now confirm that the association between Asp 57-DQB1 alleles and IDDM, previously reported in ethnically diverse cohorts collected in Western Europe, North America, and South Asia, is also present in an IDDM cohort collected in Africa.

HLA-DR and -DQ gene polymorphism in West Africans is twice as extensive as in north European Caucasians: evolutionary implications

The HLA genes are the most polymorphic coding loci known in humans. DRB-DQA-DQB gene polymorphism was investigated by Taq I restriction fragment length polymorphism analysis in more than 700 West Africans and found to be almost twice as extensive in West Africans as in North European Caucasians. This finding indicates that Africans comprise the oldest and genetically most diverse human population and supports the hypothesis of the occurrence of a population bottleneck in the emergence of the White race. As in Caucasians, less than one-third of possible cis-encoded DQA-DQB combinations were encountered, indicating constraints on the pairing of DQ alpha and beta polypeptides. Heterozygote advantage (i.e., positive selection) was found for DRB, DQA, and DQB alleles as well as for DQA-DQB combinations. However, in West Africans as well as in North Europeans the observed frequencies of DRB-DQA-DQB homozygotes were close to neutrality expectations. Although the hypothesis that HLA polymorphism is maintained by parasite-driven overdominant selection is attractive, there is little evidence to support that view. We propose instead that one of the forces maintaining a low frequency of HLA homozygotes might be a decreased likelihood of potentially autoreactive T-cell clones escaping thymic selection in HLA heterozygotes. This would be consistent with the central role of HLA molecules as self/non-self discriminators.

Common west African HLA antigens are associated with protection from severe malaria

A large case-control study of malaria in West African children shows that a human leucocyte class I antigen (HLA-Bw53) and an HLA class II haplotype (DRB1*1302-DQB1*0501), common in West Africans but rare in other racial groups, are independently associated with protection from severe malaria. In this population they account for as great a reduction in disease incidence as the sickle-cell haemoglobin variant. These data support the hypothesis that the extraordinary polymorphism of major histocompatibility complex genes has evolved primarily through natural selection by infectious pathogens.

HLA class I typing by PCR: HLA-B27 and an African B27 subtype

We describe a rapid method of HLA class I typing using the polymerase chain reaction and oligonucleotide hybridisation that eliminates the requirements for viable lymphocytes and allows subtypes to be defined. We have used this to demonstrate that the predominant subtype of HLA-B27 in the Gambia, West Africa, is HLA-B*2703, which is very rare or absent in other racial groups. This subtype differs from the common Caucasian HLA-B27 subtypes in its recognition by cytotoxic T cells. We propose that HLA*B-2703, unlike other HLA-B27 subtypes, may not be associated with ankylosing spondylitis, thus accounting in part for the rarity of this condition in black populations.

Sequence analysis of HLA-Bw53, a common West African allele, suggests an origin by gene conversion of HLA-B35

In the West African population of the Gambia the class I antigen HLA-Bw53 is found at high frequency. We used the polymerase chain reaction to amplify cDNA from an individual homozygous for this allele and determined the nucleotide sequence of the polymorphic alpha 1 and alpha 2 domains. The HLA-Bw53 sequence is identical to HLA-B35 except for a short sequence at the 3' end of exon 2 (encoding the alpha 1 domain) which specifies a Bw4 rather than a Bw6 motif. This suggests an origin for HLA-Bw53 involving a gene conversion of HLA-B35 by an allele containing this Bw4 sequence. The alpha 2 domain shared by HLA-Bw53, -B35, and -Bw58 is particularly common in sub-Saharan Africans.

HLA frequencies in black Zimbabweans

One-hundred-and-nineteen normal Black Zimbabweans were typed for HLA antigens. We found a close similarity between the HLA antigen frequencies in Zimbabweans and Black South Africans (Xhosa), another Bantu-speaking group. The only significant differences noted were for HLA-Aw36, -Bw53, -Cw6, -DR4 and -DQw3 (p less than 0.01). The most common HLA haplotypes in significant positive linkage disequilibrium in the two groups were different. The differences that were noted may be due to gene flow from the San to the Black South Africans, since it is thought that the Zimbabweans had little if any contact with the San.

HLA class II typing by digestion of PCR-amplified DNA with allele-specific restriction endonucleases will fail to unequivocally identify the genotypes of many homozygous and heterozygous individuals

Recently, a new technique for HLA class II genotyping has been introduced, the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, claimed to be a practical alternative to conventional serological and cellular HLA class II typing (1-3). The PCR-RFLP technique is ingenious, relatively rapid and does not require hybridization with sequence-specific oligonucleotide probes. However, analysis of whether homozygous and heterozygous combinations of PCR-RFLP patterns for the various investigated HLA class II loci are unique or not unfortunately shows that only 19% of DRB homozygous and heterozygous combinations are unique. The figures for the DQA1, DQB and DPB loci are 56%, 29% and 65%, respectively. As not all nucleotide sequences analyzed in the above-mentioned studies (1-3) gave rise to unique PCR-RFLPs and as more sequences now are known, for the DRB1, DRB3, DRB5 and DPB1 loci (4), the frequencies of unique PCR-RFLP patterns for the different HLA class II loci will be reduced even further. Thus, the present analysis demonstrates that the PCR-RFLP technique, performed as described in references 1-3, is not yet ready to be used for routine HLA class II genotyping. The resolution of the PCR-RFLP method can be improved by various modifications. However, the role of a modified PCR-RFLP technique in HLA class II typing still remains to be shown.

The HLA genetic constitution of the Bushmen (San)

The HLA-A, -B, and -C antigens of 290 and the DR antigens of 212 !Kung San individuals were characterized. The most frequent antigens were HLA-A30 [gene frequency (gf) = 0.193], Bw58 (gf = 0.303), Cw6 (gf = 0.327), DR4 (gf = 0.273), and DQw3 (gf = 0.553). An unexpected finding was the low frequency of the classic African black antigen Bw42 (gf = 0.004). Marked differences as well as similarities in HLA gene frequencies were observed between the San and the South African Negroes, supporting the view that they had a common origin and were then separated for a very long time. During this period differences developed as a result of selective advantage in the Negroes following the pastoralist-agriculturalist way of life as opposed to the hunter-gatherer way of life. The picture is further complicated by the fact that gene flow, mostly from the San to the southern African Negroes, took place when they met again a few hundred years ago. The data also illustrate HLA haplotypes, linkage disequilibria, and four-locus haplotypes not previously seen in other human populations. The most frequent four-locus haplotype in the San, HLA-Aw43,Cw7,B7,DRw6 was also different from A30, Cw2,Bw42,DR3, the most common among the South African Negroes.

Phenotypic expression of the HLA linked iron-loading gene in males over the age of 40 years: a population study using serial serum ferritin estimations

The frequency of the HLA linked iron-loading gene was assessed in 1783 Afrikaner men over the age of 40 years living in the South Western Cape. Measurements, made on three occasions over a 4.5 year period, included the serum ferritin concentration, a screening test for reduced unsaturated iron-binding capacity and the percentage transferrin saturation. The serum gamma-glutamyl transferase concentration was used as a marker of alcohol abuse. The diagnosis of homozygosity was based on a serum ferritin concentration that was persistently greater than 400 micrograms l-1 and a percentage transferrin saturation greater than 55%. Using these criteria, 17 subjects were diagnosed as homozygous, corresponding to a disease frequency of 0.0095, a gene frequency of 0.0976 and a heterozygote frequency of 0.176 (95% confidence limits: 0.135-0.213). None of the subjects had overt clinical haemochromatosis. Typing for the HLA-A, -B, -C and -DR loci showed that the HLA-A3 allele (frequency 0.6471 and relative risk 4.4) was the only independent marker for the iron-loading gene in this asymptomatic population. Using the present approach it was not possible to distinguish between heterozygotes, alcohol abusers and normal subjects with serum ferritin concentrations at the upper end of the normal range.

New HLA-DR2-related specificities detected in South African blacks and individuals of mixed ancestry

This study describes a new HLA-DR2-related specificity DR2LUM (CT) present in South African Blacks and individuals of mixed ancestry (Cape Coloureds). It can be distinguished from the "classic" DR2 specificities. DRw15 and DRw16, using serological and Southern blot techniques. Although no HLA-Dw specificity could be assigned to the DR2LUM(CT) cells, borderline typing reactions with Dw2 HTCs were observed. Southern blot analysis using a DRB probe and the TaqI enzyme has shown that DR2LUM(CT) shared a 1.6 kb fragment with DRw15 and a 4.7 kb fragment with DR1 and DRw10, indicating sequence homology between DR2LUM(CT) and these alleles. In addition, another unusual HLA-DR2 haplotype was found. The DR antigen was typed serologically as DRw16 but showed a combination of restriction fragments which are associated with both the DRw15 and DRw16 specificities. This study demonstrates the value of investigating non-Caucasoid populations in further characterizing the polymorphisms of the HLA class II genes.

Analysis of MHC class II DNA polymorphisms in Negroid subjects

Study of the MHC class II region is complicated by strong linkage disequilibrium between DR and DQ. Comparison of DR-DQ haplotypes between different races partly resolves this problem. We present the results of an analysis of DRB, DQA and DQB restriction fragment length polymorphisms in serologically DR-typed subjects of Negroid origin. Clearly distinguishable DRB RFLPs were observed for DR1,2,5,7 and w8. DR4,9 and w10 were uncommon in this group. DR3 was associated with two extended haplotypes, one characterised by the DQw4 allele, the other by the DQw2 allele. A recently recognised DQB RFLP (DQB 2c) was associated with DR7 and also occurred on DR5 and DR9 haplotypes. Both DR5 and DRw6 were heterogeneous in their DR-DQ relationships. Negroid subjects exhibit DR-DQ relationships distinct from other races. These provide scope for further study of MHC class II associations with disease.

Restriction fragment length polymorphism of HLA-DRw53 detected in South African blacks and individuals of mixed ancestry

The HLA-DRw53 specificity has not until now been shown to demonstrate polymorphism. We have studied 33 DRw53 haplotypes, comprising 19 DR4, 10 DR7, and 4 DR9 haplotypes, from 6 homozygous typing cells, 11 families, and 8 random individuals. All the subjects studied were South African blacks or of mixed ancestry (Cape Coloureds), with the exception of four homozygous typing cells from whites. The DNA was digested with TaqI and, after Southern blotting, was hybridized with a full-length DRB cDNA probe. Fragments correlating with DR4 (5.5 kb), DR7 (4.0 kb), and DR9 (4.1 kb) were observed. Two fragments of 14.5 and 2.8 kb correlated with DRw53. In addition, two pairs of fragments demonstrated a diallelic pattern, which is likely to correlate with a polymorphism of the DRB4 (DRw53) gene, since one or other of the two patterns was observed in all cells carrying the DRw53 specificity. The first allelic pattern, called DRw53a, was characterized by the presence of 7.5- and 2.6-kb fragments, while the second pattern, called DRw53b, had 5.8- and 2.7-kb fragments. DRw53a occurred in 10 of the 19 DR4 haplotypes and 7 of the 10 DR7 haplotypes. All three DR9,DQw2 haplotypes were also associated with DRw53a. These findings may have important implications for disease associations and the use of unrelated donors for organ transplantation.

The polymorphism of HLA-DR3 in South African populations

The polymorphism of HLA-DR3 was investigated in families and unrelated individuals of three population groups: South African (SA) Negroes, Cape Coloureds and SA Caucasoids. Serological and restriction fragment length polymorphism (RFLP) analysis indicated that DR3 could be subdivided into DRw17 (previously DR3.1) and DRw18 (previously DR3.2). In contrast, the two-dimensional (2-D) gel electrophoresis patterns could not distinguish between the DRB1 gene products of the HLA-DRw17 and DRw18 cells. Two DRB3 variants, correlating with the T-cell defined specificities Dw24 and Dw25 were identified at the genomic and product level. Of ten haplotypes studied with the newly defined HLA-DRw18 specificity, all had the DRB3 RFLP pattern associated with Dw24. HLA-DRw17 was found in all three population groups tested, although in the SA Negroes HLA-DRw18 was the prevalent DR3 subgroup. This subgroup was also present in the Cape Coloureds but was absent in the SA Caucasoids tested. HLA-DRw18 forms part of the most characteristic SA Negro haplotype, Bw42, DQw4, Dw"RSH," while HLA-DRw17 is part of the classic Caucasoid haplotype, B8, DQw2, Dw3.

HLA genotypes and variant alleles in Sudanese families of Arab-Negroid tribal origin

The indigenous population of the Blue Nile Province, Sudan, is an Arab-Negroid admixture, although some isolates of west African origin (Fallata) have begun to intermix with the indigenous population. Consanguineous marriages are common in these Muslim families. Members of 22 nuclear families were typed for HLA class I and II antigens using complement-dependent microcytotoxicity with Ninth International Workshop (9th WS) and local reagents. Considerable polymorphism was observed at each locus with a majority of the World Health Organization (WHO)-recognized alleles represented in the parental sample, albeit at low frequency. Seven parental haplotypes carried A locus alleles which were not identical to WHO-recognized specificities. All appeared to be Aw19-related specificities. Five B locus serologic variants were observed; all appeared distinct from WHO-recognized specificities. In one family we observed a new DR-DQ association; DR4 segregated with DQw2, rather than with DQw3. As has been observed for several other genetic systems in these tribes, considerable polymorphism was found for all class I and class II gene products in spite of a high level of consanguinity. Tribal admixture and/or a selective advantage in protecting the population against disease may account for this unexpectedly high level of heterozygosity.

HLA-Dw 'RSH': a new HLA-Dw specificity associated with HLA-DRw18(3)

The present study describes a new HLA-Dw specificity, Dw'RSH'. HLA-Dw'RSH' is associated with DRw18(3) and is clearly different to the DRw17(3) associated specificity Dw3. Dw'RSH' was shown to be the most common Dw specificity found in the South African (SA) Negroes (gf = 0.10) and was less common in Cape Coloureds (gf = 0.01). The specificity was absent in the SA Caucasoids tested. Dw'RSH' is part of the common Negro haplotype Bw42, DRw18, DQw4 which is seen as commonly in the SA Negroes as the B8, DRw17, DQw2, Dw3 haplotype is seen in the Caucasoids.

Definition of the HLA-Aw43 antigen

The HLA antigen Aw43 has been observed only in Southern African populations. In order to confirm its identity and clarify its definition, ten cells with this specificity were shipped to laboratories in England, the United States of America and Australia to be tested with the sera from the 10th International Histocompatibility Workshop. The results of tests on nine of these cells which were sufficiently viable indicated that HLA-Aw43 is a distinct serological specificity which could be distinguished from both the A10 cross-reacting group (A25, A26 and Aw34) and A29. The Aw43 specificity segregated in two South African Negro families, and occurred commonly in association with Bw70. The occurrence of HLA-Aw43 in South African Caucasoids, in contrast to its absence in other Caucasoid groups, is probably due to genetic admixture with indigenous South African populations.